LIPIcs, Volume 88
WABI 2017, August 21-23, 2017, Boston, MA, USA
Editors: Russell Schwartz and Knut Reinert
Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@Proceedings{schwartz_et_al:LIPIcs.WABI.2017, title = {{LIPIcs, Volume 88, WABI'17, Complete Volume}}, booktitle = {17th International Workshop on Algorithms in Bioinformatics (WABI 2017)}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-050-7}, ISSN = {1868-8969}, year = {2017}, volume = {88}, editor = {Schwartz, Russell and Reinert, Knut}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017}, URN = {urn:nbn:de:0030-drops-78120}, doi = {10.4230/LIPIcs.WABI.2017}, annote = {Keywords: Nonnumerical Algorithms and Problems, Pattern Matching, Algorithms, Life and Medical Sciences} }
Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 0:i-0:xiv, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@InProceedings{schwartz_et_al:LIPIcs.WABI.2017.0, author = {Schwartz, Russell and Reinert, Knut}, title = {{Front Matter, Table of Contents, Preface, List of Authors}}, booktitle = {17th International Workshop on Algorithms in Bioinformatics (WABI 2017)}, pages = {0:i--0:xiv}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-050-7}, ISSN = {1868-8969}, year = {2017}, volume = {88}, editor = {Schwartz, Russell and Reinert, Knut}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.0}, URN = {urn:nbn:de:0030-drops-76348}, doi = {10.4230/LIPIcs.WABI.2017.0}, annote = {Keywords: Front Matter, Table of Contents, Preface, List of Authors} }
Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
Bahar Alipanahi, Leena Salmela, Simon J. Puglisi, Martin Muggli, and Christina Boucher. Disentangled Long-Read De Bruijn Graphs via Optical Maps. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 1:1-1:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@InProceedings{alipanahi_et_al:LIPIcs.WABI.2017.1, author = {Alipanahi, Bahar and Salmela, Leena and Puglisi, Simon J. and Muggli, Martin and Boucher, Christina}, title = {{Disentangled Long-Read De Bruijn Graphs via Optical Maps}}, booktitle = {17th International Workshop on Algorithms in Bioinformatics (WABI 2017)}, pages = {1:1--1:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-050-7}, ISSN = {1868-8969}, year = {2017}, volume = {88}, editor = {Schwartz, Russell and Reinert, Knut}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.1}, URN = {urn:nbn:de:0030-drops-76614}, doi = {10.4230/LIPIcs.WABI.2017.1}, annote = {Keywords: Positional de Bruijn graph, Genome Assembly, Long Read Data, Optical maps} }
Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
Md. Shamsuzzoha Bayzid and Tandy Warnow. Gene Tree Parsimony for Incomplete Gene Trees. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 2:1-2:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@InProceedings{bayzid_et_al:LIPIcs.WABI.2017.2, author = {Bayzid, Md. Shamsuzzoha and Warnow, Tandy}, title = {{Gene Tree Parsimony for Incomplete Gene Trees}}, booktitle = {17th International Workshop on Algorithms in Bioinformatics (WABI 2017)}, pages = {2:1--2:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-050-7}, ISSN = {1868-8969}, year = {2017}, volume = {88}, editor = {Schwartz, Russell and Reinert, Knut}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.2}, URN = {urn:nbn:de:0030-drops-76495}, doi = {10.4230/LIPIcs.WABI.2017.2}, annote = {Keywords: Gene duplication and loss, gene tree parsimony, deep coalescence} }
Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
Brian Brubach, Jay Ghurye, Mihai Pop, and Aravind Srinivasan. Better Greedy Sequence Clustering with Fast Banded Alignment. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 3:1-3:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@InProceedings{brubach_et_al:LIPIcs.WABI.2017.3, author = {Brubach, Brian and Ghurye, Jay and Pop, Mihai and Srinivasan, Aravind}, title = {{Better Greedy Sequence Clustering with Fast Banded Alignment}}, booktitle = {17th International Workshop on Algorithms in Bioinformatics (WABI 2017)}, pages = {3:1--3:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-050-7}, ISSN = {1868-8969}, year = {2017}, volume = {88}, editor = {Schwartz, Russell and Reinert, Knut}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.3}, URN = {urn:nbn:de:0030-drops-76425}, doi = {10.4230/LIPIcs.WABI.2017.3}, annote = {Keywords: Sequence Clustering, Metagenomics, String Algorithms} }
Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
Yannis Almirantis, Panagiotis Charalampopoulos, Jia Gao, Costas S. Iliopoulos, Manal Mohamed, Solon P. Pissis, and Dimitris Polychronopoulos. Optimal Computation of Overabundant Words. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 4:1-4:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@InProceedings{almirantis_et_al:LIPIcs.WABI.2017.4, author = {Almirantis, Yannis and Charalampopoulos, Panagiotis and Gao, Jia and Iliopoulos, Costas S. and Mohamed, Manal and Pissis, Solon P. and Polychronopoulos, Dimitris}, title = {{Optimal Computation of Overabundant Words}}, booktitle = {17th International Workshop on Algorithms in Bioinformatics (WABI 2017)}, pages = {4:1--4:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-050-7}, ISSN = {1868-8969}, year = {2017}, volume = {88}, editor = {Schwartz, Russell and Reinert, Knut}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.4}, URN = {urn:nbn:de:0030-drops-76468}, doi = {10.4230/LIPIcs.WABI.2017.4}, annote = {Keywords: overabundant words, avoided words, suffix tree, DNA sequence analysis} }
Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
Michal Aleksander Ciach, Anna Muszewska, and Pawel Górecki. Detecting Locus Acquisition Events in Gene Trees. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 5:1-5:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@InProceedings{ciach_et_al:LIPIcs.WABI.2017.5, author = {Ciach, Michal Aleksander and Muszewska, Anna and G\'{o}recki, Pawel}, title = {{Detecting Locus Acquisition Events in Gene Trees}}, booktitle = {17th International Workshop on Algorithms in Bioinformatics (WABI 2017)}, pages = {5:1--5:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-050-7}, ISSN = {1868-8969}, year = {2017}, volume = {88}, editor = {Schwartz, Russell and Reinert, Knut}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.5}, URN = {urn:nbn:de:0030-drops-76545}, doi = {10.4230/LIPIcs.WABI.2017.5}, annote = {Keywords: rank, taxon, ranked species tree, speciation, gene duplication, gene loss, horizontal gene transfer} }
Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
Amir H. Bayegan and Peter Clote. An IP Algorithm for RNA Folding Trajectories. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 6:1-6:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@InProceedings{bayegan_et_al:LIPIcs.WABI.2017.6, author = {Bayegan, Amir H. and Clote, Peter}, title = {{An IP Algorithm for RNA Folding Trajectories}}, booktitle = {17th International Workshop on Algorithms in Bioinformatics (WABI 2017)}, pages = {6:1--6:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-050-7}, ISSN = {1868-8969}, year = {2017}, volume = {88}, editor = {Schwartz, Russell and Reinert, Knut}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.6}, URN = {urn:nbn:de:0030-drops-76437}, doi = {10.4230/LIPIcs.WABI.2017.6}, annote = {Keywords: Integer programming, RNA secondary structure, folding trajectory, feedback vertex problem, conflict digraph} }
Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
Samuele Girotto, Matteo Comin, and Cinzia Pizzi. Fast Spaced Seed Hashing. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 7:1-7:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@InProceedings{girotto_et_al:LIPIcs.WABI.2017.7, author = {Girotto, Samuele and Comin, Matteo and Pizzi, Cinzia}, title = {{Fast Spaced Seed Hashing}}, booktitle = {17th International Workshop on Algorithms in Bioinformatics (WABI 2017)}, pages = {7:1--7:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-050-7}, ISSN = {1868-8969}, year = {2017}, volume = {88}, editor = {Schwartz, Russell and Reinert, Knut}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.7}, URN = {urn:nbn:de:0030-drops-76501}, doi = {10.4230/LIPIcs.WABI.2017.7}, annote = {Keywords: k-mers, spaced seeds, efficient hashing} }
Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
Nadia El-Mabrouk and Aïda Ouangraoua. A General Framework for Gene Tree Correction Based on Duplication-Loss Reconciliation. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 8:1-8:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@InProceedings{elmabrouk_et_al:LIPIcs.WABI.2017.8, author = {El-Mabrouk, Nadia and Ouangraoua, A\"{i}da}, title = {{A General Framework for Gene Tree Correction Based on Duplication-Loss Reconciliation}}, booktitle = {17th International Workshop on Algorithms in Bioinformatics (WABI 2017)}, pages = {8:1--8:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-050-7}, ISSN = {1868-8969}, year = {2017}, volume = {88}, editor = {Schwartz, Russell and Reinert, Knut}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.8}, URN = {urn:nbn:de:0030-drops-76565}, doi = {10.4230/LIPIcs.WABI.2017.8}, annote = {Keywords: Gene tree correction, Supertree, Polytomy, Reconciliation, Phylogeny} }
Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
Maxime Crochemore, Alexandre P. Francisco, Solon P. Pissis, and Cátia Vaz. Towards Distance-Based Phylogenetic Inference in Average-Case Linear-Time. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 9:1-9:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@InProceedings{crochemore_et_al:LIPIcs.WABI.2017.9, author = {Crochemore, Maxime and Francisco, Alexandre P. and Pissis, Solon P. and Vaz, C\'{a}tia}, title = {{Towards Distance-Based Phylogenetic Inference in Average-Case Linear-Time}}, booktitle = {17th International Workshop on Algorithms in Bioinformatics (WABI 2017)}, pages = {9:1--9:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-050-7}, ISSN = {1868-8969}, year = {2017}, volume = {88}, editor = {Schwartz, Russell and Reinert, Knut}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.9}, URN = {urn:nbn:de:0030-drops-76529}, doi = {10.4230/LIPIcs.WABI.2017.9}, annote = {Keywords: computational biology, phylogenetic inference, Hamming distance} }
Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
Mohamed K. Gunady, Steffen Cornwell, Stephen M. Mount, and Héctor Corrada Bravo. Yanagi: Transcript Segment Library Construction for RNA-Seq Quantification. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 10:1-10:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@InProceedings{gunady_et_al:LIPIcs.WABI.2017.10, author = {Gunady, Mohamed K. and Cornwell, Steffen and Mount, Stephen M. and Bravo, H\'{e}ctor Corrada}, title = {{Yanagi: Transcript Segment Library Construction for RNA-Seq Quantification}}, booktitle = {17th International Workshop on Algorithms in Bioinformatics (WABI 2017)}, pages = {10:1--10:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-050-7}, ISSN = {1868-8969}, year = {2017}, volume = {88}, editor = {Schwartz, Russell and Reinert, Knut}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.10}, URN = {urn:nbn:de:0030-drops-76487}, doi = {10.4230/LIPIcs.WABI.2017.10}, annote = {Keywords: RNA-Seq, Genome Sequencing, Kmer-based alignment, Transcriptome Quantification, Differential Alternative Splicing} }
Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
Chenyue W. Hu, Hanyang Li, and Amina A. Qutub. Shrinkage Clustering: A Fast and Size-Constrained Algorithm for Biomedical Applications. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 11:1-11:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@InProceedings{hu_et_al:LIPIcs.WABI.2017.11, author = {Hu, Chenyue W. and Li, Hanyang and Qutub, Amina A.}, title = {{Shrinkage Clustering: A Fast and Size-Constrained Algorithm for Biomedical Applications}}, booktitle = {17th International Workshop on Algorithms in Bioinformatics (WABI 2017)}, pages = {11:1--11:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-050-7}, ISSN = {1868-8969}, year = {2017}, volume = {88}, editor = {Schwartz, Russell and Reinert, Knut}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.11}, URN = {urn:nbn:de:0030-drops-76556}, doi = {10.4230/LIPIcs.WABI.2017.11}, annote = {Keywords: Clustering, Matrix Factorization, Cancer Subtyping, Gene Expression} }
Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
Hosna Jabbari, Ian Wark, Carlo Montemagno, and Sebastian Will. Sparsification Enables Predicting Kissing Hairpin Pseudoknot Structures of Long RNAs in Practice. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 12:1-12:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@InProceedings{jabbari_et_al:LIPIcs.WABI.2017.12, author = {Jabbari, Hosna and Wark, Ian and Montemagno, Carlo and Will, Sebastian}, title = {{Sparsification Enables Predicting Kissing Hairpin Pseudoknot Structures of Long RNAs in Practice}}, booktitle = {17th International Workshop on Algorithms in Bioinformatics (WABI 2017)}, pages = {12:1--12:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-050-7}, ISSN = {1868-8969}, year = {2017}, volume = {88}, editor = {Schwartz, Russell and Reinert, Knut}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.12}, URN = {urn:nbn:de:0030-drops-76408}, doi = {10.4230/LIPIcs.WABI.2017.12}, annote = {Keywords: RNA, secondary structure prediction, pseudoknots, space efficiency, sparsification} }
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